I finally got my software to work. (Only tested on one data-set so far).
What initially fooled me was that the pointcloud viewer I used (CloudCompare) actually reversed the east coordinates, so that the pointcloud was displayed mirrored.
With regard to Photosynth coordinate system, what I found to work was;
North => (0, 1, 0)
East => (-1, 0, 0)
Elev =) (0, 0, 1)
(Which probably is the same as douglas described, map/pointcloud just rotated 180 deg about the elev/Z-axis).